I put everything back together carefully. The ATX IO shield was loose. I remember a loose shield touching the edge of a motherboard causing shorts a long time ago. I pushed it in carefully. This minuet case is a pleasure to work on compared to the AST LPX case I was working with last week. That case found a way to slice my fingers on a daily basis. So much bleeding. Hard to use your phone with bandages on both thumbs! The AM2 board that used to be in the case had 8 screws holding it in. New board is shorter and only touched 6 of the stands. I counted 9 screws. So I think that answers the cause of the short. One of the hard drive screws must have been in there.
The motherboard still works, but the onboard video has a very purple tint. I think I know what got damaged now.
Had a hard time finding a storage device that works with the UDMA enabled. Kingston 16GB MSata works. Windows 98 is installing. Blessedly, the motherboard supports booting from CD-ROM, because installing from floppies wasn't going to be fun and I had trouble
And I'm whipping up a second set of 3d printed low profile brackets. Turns out that low profile brackets are mirror images of full height. Did not know that.
Since it seems like I got the onboard UDMA to working, I've got the two cards picked out:
1) Geforce 4000MX, because I got one, and the integrated video output seems messed up.
2) NEC based USB 2.0 card, because I want to wire up the front panel. The completionist in me wishes I had firewire too, but I if I have to skip something, that would be it.